| 2026 | MFCS | A Congestion Parameter for Depth-First Graph Traversals. | Codaline Bourotte, Gwendal Ducloz, Pekka Orponen, Shinnosuke Seki |
| 2025 | DNA | Programmable Co‑Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion. | Da-Jung Cho, Szilrd Zsolt Fazekas, Shinnosuke Seki, Max Wiedenhft |
| 2025 | DNA | Secondary Structure Design for Cotranscriptional 3D RNA Origami Wireframes. | Pekka Orponen, Shinnosuke Seki, Antti Elonen |
| 2022 | ISAAC | On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding. | Szilrd Zsolt Fazekas, Hwee Kim, Ryuichi Matsuoka, Shinnosuke Seki, Hinano Takeuchi |
| 2022 | STACS | Oritatami Systems Assemble Shapes No Less Complex Than Tile Assembly Model (ATAM). | Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Guillaume Theyssier |
| 2020 | LATIN | Simple Intrinsic Simulation of Cellular Automata in Oritatami Molecular Folding Model. | Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Yuki Ubukata |
| 2020 | SOFSEM | Counting Infinitely by Oritatami Co-transcriptional Folding. | Kohei Maruyama, Shinnosuke Seki |
| 2019 | DLT | Single-Stranded Architectures for Computing. | Shinnosuke Seki |
| 2019 | TAMC | On the Power of Oritatami Cotranscriptional Folding with Unary Bead Sequence. | Szilrd Zsolt Fazekas, Kohei Maruyama, Reoto Morita, Shinnosuke Seki |
| 2018 | DNA | Know When to Fold 'Em: Self-assembly of Shapes by Folding in Oritatami. | Erik D. Demaine, Jacob Hendricks, Meagan Olsen, Matthew J. Patitz, Trent A. Rogers, Nicolas Schabanel, Shinnosuke Seki, Hadley Thomas |
| 2018 | DNA | Transcript Design Problem of Oritatami Systems. | Yo-Sub Han, Hwee Kim, Shinnosuke Seki |
| 2018 | ISAAC | Proving the Turing Universality of Oritatami Co-Transcriptional Folding. | Cody W. Geary, Pierre-tienne Meunier, Nicolas Schabanel, Shinnosuke Seki |
| 2016 | DNA | Nondeterministic Seedless Oritatami Systems and Hardness of Testing Their Equivalence. | Yo-Sub Han, Hwee Kim, Makoto Ota, Shinnosuke Seki |
| 2016 | MFCS | Programming Biomolecules That Fold Greedily During Transcription. | Cody W. Geary, Pierre-Etienne Meunier, Nicolas Schabanel, Shinnosuke Seki |
| 2015 | ICALP | Binary Pattern Tile Set Synthesis Is NP-hard. | Lila Kari, Steffen Kopecki, Pierre-tienne Meunier, Matthew J. Patitz, Shinnosuke Seki |
| 2014 | MFCS | Generalised Lyndon-Schtzenberger Equations. | Florin Manea, Mike Mller, Dirk Nowotka, Shinnosuke Seki |
| 2014 | SOFSEM | A Stronger Square Conjecture on Binary Words. | Natasa Jonoska, Florin Manea, Shinnosuke Seki |
| 2013 | DNA | 3-Color Bounded Patterned Self-assembly - (Extended Abstract). | Lila Kari, Steffen Kopecki, Shinnosuke Seki |
| 2013 | ISAAC | Computing Minimum Tile Sets to Self-Assemble Color Patterns. | Aleck C. Johnsen, Ming-Yang Kao, Shinnosuke Seki |
| 2013 | TAMC | On the Boundedness Property of Semilinear Sets. | Oscar H. Ibarra, Shinnosuke Seki |
| 2013 | UC | Combinatorial Optimization in Pattern Assembly - (Extended Abstract). | Shinnosuke Seki |
| 2012 | CiE | On the Behavior of Tile Assembly System at High Temperatures. | Shinnosuke Seki, Yasushi Okuno |
| 2012 | DLT | Converting Nondeterministic Automata and Context-Free Grammars into Parikh Equivalent Deterministic Automata. | Giovanna J. Lavado, Giovanni Pighizzini, Shinnosuke Seki |
| 2012 | SOFSEM | Iterated Hairpin Completions of Non-crossing Words. | Lila Kari, Steffen Kopecki, Shinnosuke Seki |
| 2011 | ISAAC | Program Size and Temperature in Self-Assembly. | Ho-Lin Chen, David Doty, Shinnosuke Seki |
| 2011 | SODA | The Power of Nondeterminism in Self-Assembly. | Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki |
| 2011 | SOFSEM | One-Reversal Counter Machines and Multihead Automata: Revisited. | Ehsan Chiniforooshan, Mark Daley, Oscar H. Ibarra, Lila Kari, Shinnosuke Seki |
| 2010 | DLT | Schema for Parallel Insertion and Deletion. | Lila Kari, Shinnosuke Seki |
| 2010 | DNA | Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement. | Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki |
| 2010 | DNA | Triangular Tile Self-assembly Systems. | Lila Kari, Shinnosuke Seki, Zhi Xu |
| 2009 | DLT | An Extension of the Lyndon Schtzenberger Result to Pseudoperiodic Words. | Elena Czeizler, Eugen Czeizler, Lila Kari, Shinnosuke Seki |
| 2008 | DLT | Duplication in DNA Sequences. | Masami Ito, Lila Kari, Zachary Kincaid, Shinnosuke Seki |
| 2008 | MFCS | On a Special Class of Primitive Words. | Elena Czeizler, Lila Kari, Shinnosuke Seki |